coot_tutorial

• activate ccp4 commands: type in terminal -> ccp4
• open coot: type in terminal -> vglrun coot
• load data tutorial: calculate -> Load tutorial model and data (sometimes is in Extensions)
• set sphere radius in which 3D map is shown: edit -> map parameters -> map radius -> 16
• change steps: general - smooth recentering- 10
• verbose icos: general - refinement tool bar - icos and text
• Navigation:
  • Left-mouse Drag Rotate view
  • Ctrl Left-Mouse Drag Translates view
  • Shift Left-Mouse Label Atom
  • Right-Mouse Drag Zoom in and out
  • Middle-mouse Centre on atom
  • Scroll-wheel Forward Increase map contour level
  • Scroll-wheel Backward Decrease map contour level
• Set background color to white (good for papers): Edit → Background Colour → White
• Improve speed
  • Edit → Preferences…
  • Smooth Recentering → 10 steps {smaller numbers are quicker}
• Go To Residue: CTRL-G 23A (goes to residue 23 in chain A)
• You can toggle spin and rock the view with: C%TRL-R
• Validate:
  • Ramachandran (https://www.quora.com/What-is-a-Ramachandran-plot-1)
  • Density Fit
  • Geometry
• RC constrains
• Fix: 89A, 41A
• calculate -> model (icon with text)
• set all constrains
• Icon:
  • Real space refine
  • Rigid body
  • Rotamer
  • Mutate
  • Add residue
• validate: ramachandran, rotamer, density probe ====== Assignment
• load data tutorial: calculate -> Load tutorial model and data (sometimes is in Extensions)
• open validate, ramachandran, rotamer, density probe
• fix problem (real space refine zone, rotamers, mutate/delete)